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Series GSE5407 Query DataSets for GSE5407
Status Public on Jul 31, 2006
Title Comparative transcript profiling of interaction events in Pinus sylvestris root tissues following challenge (15dpi).
Platform organism Pinus taeda
Sample organism Pinus sylvestris
Experiment type Expression profiling by array
Summary The response mechanisms, recognition and specificity of conifer trees during interaction with pathogenic, saprotrophic or symbiotic ectomycorrhizal fungus were investigated. The roots of Pinus sylvestris were challenged for fifteen days with either Heterobasidion annosum (a pathogenic root rot fungus which attacks Norway spruce, Scots pine and broad leaf trees); Laccaria bicolor (an obligate ectomycorrhizal symbiont); or Trichoderma aureoviride (an obligate saprotroph). The gene expression data from cDNA micro-arrays consisting of 2176 Pinus taeda genes were analysed using 2-interconnected mixed linear model statistical approach. The result of the pairwise comparisons of the different treatments against un-inoculated control led to identification of genes specifically differentially expressed in the pathogenic, saprotrophic and symbiotic interactions. The results were compared with similar data obtained for two other interaction stages: 1 and 5 days post inoculation. The result of this comprehensive expression profiling will hopefully shed more light on the mechanistic basis for recognition and response of conifer trees to pathogenic and non-pathogenic fungi.
Keywords: stress response
 
Overall design Three replicates (A,B, and C) of 12 arrays each. In each replicate each of the 4 samples is paired with each of the other 3 samples in both dye assignment possibilities (i.e. a dye-swap is performed).
 
Contributor(s) Heller G, Adomas A, Li G, Olson A, Osborne J, Craig D, van Zyl L, Sederoff R, Dean RA, Stenlid J, Finlay R, Asiegbu FO
Citation(s) 17669735, 18381269, 18298811
Submission date Jul 28, 2006
Last update date Apr 01, 2020
Contact name Chris Smith
Organization name NCSU
Department Bioinformatics Research Center
Lab 1500 Partners II
Street address 840 Main Campus Dr
City Raleigh
State/province NC
ZIP/Postal code 27606
Country USA
 
Platforms (1)
GPL4039 Pinus taeda cDNA
Samples (36)
GSM123800 15dpi rep B Control (Cy5) vs. Mycorrhiza (Cy3) (12384124)
GSM123801 15dpi rep B Saprotroph (Cy5) vs. Mycorrhiza (Cy3) (12384127)
GSM123802 15dpi rep B Mycorrhiza (Cy5) vs. Saprotroph (Cy3) (12384128)
This SubSeries is part of SuperSeries:
GSE5410 Comparative transcriptome analysis of early interaction events in Scots pine root tissues following challenge
Relations
BioProject PRJNA104333

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE5407_RAW.tar 28.5 Mb (http)(custom) TAR (of TXT)

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